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4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 300 0.2 M Sodium malonate pH 5.0, 20% w/v Polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 3.12 60.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.045 α = 90 b = 270.201 β = 90 c = 113.627 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL RIGAKU HyPix-6000HE 2022-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.05 26.44 98.3 0.978 6.3 4.8 37226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.19 0.911
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.05 25.221 37214 1829 98.063 0.267 0.2635 0.2652 0.3352 0.3379 30.756
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.901 2.143 -0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.832 r_dihedral_angle_6_deg 14.327 r_dihedral_angle_2_deg 9.462 r_dihedral_angle_1_deg 7.584 r_lrange_it 6.815 r_rigid_bond_restr 3.979 r_scangle_it 3.482 r_mcangle_it 3.409 r_scbond_it 2.154 r_mcbond_it 2.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.832 r_dihedral_angle_6_deg 14.327 r_dihedral_angle_2_deg 9.462 r_dihedral_angle_1_deg 7.584 r_lrange_it 6.815 r_rigid_bond_restr 3.979 r_scangle_it 3.482 r_mcangle_it 3.409 r_scbond_it 2.154 r_mcbond_it 2.111 r_angle_refined_deg 1.496 r_nbtor_refined 0.318 r_nbd_refined 0.239 r_symmetry_nbd_refined 0.236 r_xyhbond_nbd_refined 0.142 r_ncsr_local_group_3 0.112 r_chiral_restr 0.111 r_ncsr_local_group_5 0.109 r_ncsr_local_group_6 0.105 r_ncsr_local_group_1 0.093 r_ncsr_local_group_2 0.084 r_ncsr_local_group_4 0.078 r_symmetry_xyhbond_nbd_refined 0.045 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10283 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing